X will gain a new weapon each time you defeat one of the eight bosses. Each weapon has its own special abilities and are certain bosses' weakness, some can also be used to retrieve certain items that are normally out of reach.

- X-Buster

The X-Buster is the standard weapon for X and you begin the game with it. Firing a normal shot is a small energy ball which causes a small amount of damage to enemies. When the X-Buster is charged up to its first level, a stronger green energy beam will fire out causing more damage to targets. The second stage is a large blue beam that causes more damage. The third stage can only be reached when the weapon upgrade powerup is found. It fires off huge purple beams which cause maximum damage from the X-Buster.

- Gained from: N/A

The special weapons can only have their secondary fire mode used when X has the X-Buster upgrade so that he can charge his X-Buster until he glows purple.

- Fire Wave

The Fire Wave weapon is gained when Flame Mammoth is defeated. The weapon's primary fire is a short-range burst of fire which can smolder targets. The charged up stage of the Fire Wave releases large flame walls which fly forward, striking any targets in the way.

- Boss: Flame Mammoth

- Shotgun Ice

The Shotgun Ice weapon is gained after you defeat Chill Penguin. This weapon's primary fire is an ice block which can either damage targets or sometimes freeze enemies. If the block hits an obstacle such as a wall, the block will break and smaller projectiles will reflect back off the wall. The charged state of the weapon creates a platform which X can ride. Once the platform is created it will slide forward for a limited time.

- Boss: Chill Penguin

- Electric Spark

The Electric Spark weapon is gained once you defeat Spark Mandrill. The weapon's primary fire will shoot out an electric spark-ball which can damage or electrocute targets. The charged state of this weapon will fire out two giant walls of electricity either side of X and can destroy any targets they strike through.

- Boss: Spark Mandrill

- Rolling Shield

The Rolling Shield is gained after you defeat Armored Armadillo. The primary fire of this weapon shoots out a large blue ball that bounces across the screen until it hits a target. If it hits a wall, it will reflect off it and continue on in the opposite direction. The charged-up state will create a defensive shield around X. This will protect him against any enemies who try to strike X. Energy projectiles will be deflected, but if a strong solid object strikes the shield it will turn off.

- Boss: Armored Armadillo

- Homing Torpedo

The Homing Torpedo weapon is gained after you defeat Launch Octopus. The primary fire of this weapon will fire out a single missile which with fly off and home in on an enemy target, destroying it or damaging it once contact is made. The secondary fire will shoot out six larger missiles and will spray them out in front of X to strike any targets in front of him.

- Boss: Launch Octopus

- Boomerang Cutter

The Boomerang Cutter weapon is gained when Boomer Kuwanger is defeated. The primary fire will shoot out a boomerang that will disappear once it hits a target or it will fly out in a circular fashion and return to X. This can be used to retrieve items out of reach. The secondary fire will fire out eight large boomerang-shaped projectiles in diagonal directions from X.

- Boss: Boomer Kuwanger

- Chameleon Sting

The Chameleon Sting weapon is gained once you defeat Sting Chameleon. The primary fire of this weapon will shoot out three green beams, two of which fire out at diagonals to X and the middle one will fire straight ahead. The secondary fire will cause X to flash, indicating that he can walk through enemies for a limited time without taking damage.

- Boss: Sting Chameleon

- Storm Tornado

The Chameleon Sting weapon is gained once you defeat Sting Chameleon. The primary fire of this weapon will shoot out three green beams, two of which fire out at diagonals to X and the middle one will fire straight ahead. The secondary fire will cause X to flash, indicating that he can walk through enemies for a limited time without taking damage.